Fig. 5

Genomic alterations of the TIME phenotypes. a Significantly mutated genes (SMGs) in three TIME phenotypes. b Mutation signatures extracted from three TIME phenotypes. c The pie chart shows the proportion of mutation signatures in three TIME phenotypes. The distribution of FGA (d), FGG (e) and FGL (f) in three TIME phenotypes. g Gain (red) or loss (blue) frequencies of copy number variations (CNVs) in the autosomes of HCC patients. h Integrated molecular comparison of genomic alterations in signaling pathways across the TIME phenotypes. Each gene box includes three percentages representing the frequency of activation or inactivation in TIME-1, 2, and 3. All changes are tallied together in calculating the percentages of altered cases within each TIME phenotype. Genomic alterations include mutations and copy-number changes. Missense mutations are only counted if they have known oncogenic function, have been reported in COSMIC, or occur at known mutational hotspots. Genes are grouped by signaling pathways, with edges showing pairwise molecular interactions. For the boxplot, the asterisks represented the statistical p value (^nsP > 0.05, *P < 0.05, **P < 0.01, *** P < 0.001, **** P < 0.0001)